Abstract: Microcystis aentginosa and Scenedesmus obliquus are the main part of algae blooms in Lake Taihu. For the purpose of identify the type and percentage of algae in algae blooms, thrice courses experiment were carried out on 16th Aug., 23th Oct., 2006 and 12th Nov., 2007, additionally, photosensitive pigment absorption signals of pure Microcystis aentginosa and Scenedesmus obliquus were measured in the laboratory. The photosensitive pigments of water samples were identified by the methods of Fourth-Derivative and standardization coefficient. Then the percentage of Microcystis aentginosa and Scenedesmus obliquus in the Taihu Lake were estimated through the match-up method of absorption signals. The results indicated that photosensitive pigment absorption signals of pure algae could be well used in the algae identification; it made a full consideration to the effect of Auxiliary pigment in identification, and gave a better method to avoid the interference of non-pigment material absorption signal. Microcystis aentginosa had the highest percentage in the wild phytoplankton population, which followed by Scenedesmus obliquus. The proportion of Microcystis aeruginosa decreased from summer to winter, while Scenedesmus obliquus increased gradually, but the percentage of Microcystis aeruginosa still slightly higher than that of Scenedesmus obliquus. The spatial variation of Microcystis aeruginosa is very small, but the temporal difference is huge, on the contrary, Scenedesmus obliquus has large spatial variation and small temporal variation.